Side Mission
by FalconWriter9000
Summary: 2B is kidnapped by a rogue android and it's up to 9S to save her. A happier ending for the game. 2Bx9S. Stronger 9S.
1. Prologue

**A Nier Automata Fanfiction cause all that I've read was tragic stories of 9s and 2B. Here it has more of a happy ending with stronger 9s.** **Disclaimer: I do not own any of the characters written in this story. They all belong to the evil creator himself.** **_**

A side mission that's all she thought it was. Three weeks ago command has assigned them to a mission regarding a rogue corrupted android that needed to be exterminated. Like the machines weren't enough as it is. She has been trapped in here for a week, a month, she couldn't tell. Her pod has been shut down. Most of her chips were also hacked and she had no way of communicating the bunker. She had no control over her body so self destructing wasn't an option. She just laid there trapped, feeling useless and broken.

This rogue android who now called himself "7", knew too much and had lost his sanity. His logic circuits weren't working and had been infected by the logic virus. He kept going on and talking about a failed project that led humanity to extinction.

XxXxXxXxXxXxXxXxXxXxXx 3 Months Ago XxXxXxXxXxXxXxXxXxXxXx

"7" was one of the operators at YoRHa. He was granted permission to report to the commander about recent news that the android assigned to him had found. While he was looking for her, he found her talking with 9s a high end scanner unit. He heard everything including the council of humanity was created by YoRHa and not the other way around and about Humanity's extinction.

This news shocked 7 to his core and he lost every hope he had. He escaped the bunker and using a stolen flying unit, traveled to earth.

His weak control over his emotions put him in a vulnerable state which risked him into getting infected by a virus. Without a pod warning him of the risk his body is in, he was infected by several viruses but they were all hacked and erased from his system. He went over a lot of emotions; anger, sadness, confusion and most of all grief. He had lost his purpose in life. His only purpose was to serve humans and if they were extinct way before they were created, that meant that everything the Commander told them was a lie.

7 found himself going through a lot of emotions that he couldn't handle. Soon his logic circuits were damaged and he lost his sanity. "By now they are looking for me, hunting for me. The battle units are coming. I should keep on moving. I will find a purpose again." with that thought in mind he kept moving. He hacked machines to get their parts so he wouldn't stay with his damaged body. He took shelter in City Ruins mostly as it had a giant sewer system under it. Since he went rogue and escaped the Bunker, he was automatically disconnected from the system which meant that he couldn't back up his data and if he died, that was it for him.

7 did not engage in unnecessary combat and when he did, it was to get spare parts and equipments to upgrade his body. Once he got his body in a stronger and better shape he started dealing with non-hostile machines. Seeing them immitate and make the same mitake as humans, he gathered and lead a bunch of them.

"I will erase the lies and the betrayers from this world. The war has done enough damage, it's time for it to end. YoRHa will be no more." 7 had found a purpose again and he will make sure to accomplish that purpose.

XxXxXxXxXxXxXxXxXxXxXxXx Two Months Later XxXxXxXxXxXxXxXxXxXxXxXxXxXxXxX

"These flowers are pretty rare you know ma'am?" said 9s as he picked a lunar tear and held it to his nose. He took a deep breath and exhaled.

" Talking about flowers, you can take a picture of this one and send it to your operator 6O. I'm sure she would be thrilled about this since this is also a pretty rare flower." suggested 9s. 2B looked at him and accepted his offer. She took a quick photo of the flower and sent it to her operator. " Let's keep moving it has been almost two months and we do not have enough clue about the rogue android." deadpanned 2B as she went ahead. "I'm sure we'll find something in the future ma'am." Said 9s.

She did not have a slightest clue how he could be so hopeful and pure in this cruel world. "Yes we're bound to find something eventually. And stop calling me ma'am." said 2B with a quick reply of "yes 2B" from 9s.

Since they thought this rogue android was an operator type, they didn't make a big deal out of it and underestimated him. They had no idea what was about to come.

End Of Prologue

 **_** **Rate and Review please and hope you enjoyed this prologue .**


	2. Chapter 1: The strange Behavior

It has been two days since me and 2B are looking for operator Seven. I can already see that 2B is getting irritated. I tried cheering her up but she keeps shutting herself out doesn't talk to me much and focuses on the mission ahead. I do not know what is causing her to be like this with me whatsoever. On the bright side it isn't affecting our mission at all in fact, we are getting better progress day by day. After a while I noticed that she is getting way ahead of me, so I walk a little faster and catch up to her.

We looked building over building for clues but the closest clue we found was that the machines kept whispering strange stuff that was out of their predictable and ordinary manner. Can't say predictable anymore as the machines are trying to imitate and act more like human beings.

Currently, we are searching over The City Ruins. We asked some of the androids in the resistance camp and they told us that most of the suspicious activities were at City Ruins. We entered a large and tall building which was very dark and I had trouble seeing. I noticed that the building was mostly covered by plants. Even in the inside there was some plant life to be seen. As 2B started looking around, I got lost in my thoughts. Day by day in this investigation I keep hearing Operator Seven's name more and more. Seven has been gaining popularity between androids. The first Operator type android or any other that managed to break out of the bunker without the commander's permission and steal a flight unit. Of course seven would be a subject that most of us wanted to talk about. Even I was curious how he managed to do it, can't say the same thing about 2B though, she only focused on what was ahead.

Some of the machines also spoke out sometimes and kept saying his name like some broken and glitchy toy doll. But strangely enough only two of them did. How would they know about seven though? Machines usually talked about their own beliefs or anything else on that matter but never did they talk about androids or a specific one in the first place. I am not feeling good about seven at all. There is something suspicious going on with him. But I dismissed this feeling so it wouldn't affect the progress of our mission. The faster we get this mission over with, the faster we can destroy the machines and win the war. Then humans can come and live on earth again. Then we would save the world and fulfill our purpose.

"Watch Out 9S!" said 2B as she slashed an upcoming machine unit that was about to crush me. Wait, how did that machine get here? Where did it come from? Why didn't I notice it? "9S!!" shouted 2B which made me come back to my senses and notice a machine shooting a laser beam at me. I quickly dodged it and slashed the machine in half with Cruel Oath. After slashing, destroying and hacking a lot of machines, me and 2B were surprised to find out that the machines still kept coming and were even more surprised that they were now too much for us to handle. They were gaining up on us and doubling their numbers, several of our options to attack were running out. Where the heck are these machines coming from and why are there so many of them? After what felt like hours of slashing and stabbing, we were feeling restraint on our joints and limbs. It was rare for androids to feel fatigue, it mostly happened when we were in a dire need for maintenance.

Regardless of how exhausted we were, we still kept fighting. The machines completely surrounded us, me and 2B's backs were against each other. "We should find a way to get out of here, there are too many and we can't handle them all at once in this closed area." I exclaimed as I looked around us. It seemed like most of them were coming from the entrance of the building. How did through the entrance of this building without me or 2B's notice?

"I agree. Let's head towards the exit." Replied 2B as she used a heavy attack and slashed 5 machines at the same time. "We can't, there is just too many machines blocking the exit and by the looks of it, it seems that they keep coming from there." I then panicked. The situation was getting more and more out of hand. "Seven-Sama" "Seven-Sama" "Seven-Sama" I heard several of the machines repeating it. At first I dismissed it until I realized that the two machines didn't see Seven as their master. They just repeat his name like some malfunctioned toy.

'Ok, calm down and analyze the situation. Me and 2B are surrounded by machines in a closed area and a very dark building. Our visors help a little but not so much.' I looked around and noticed that there are fewer machines at the end of the hall. There are also elevators there and with a little luck hopefully there should not be any room blocking the ladder going all the way up towards the tunnel. Judging the height of the building it will take us some time to get to the roof. "There! We can use the ladders inside the lift tunnels to escape these machines." I shouted while at the same time activating my wide area hacking. The machines blocking our path towards the elevator were stunned and I cut them in half with Cruel Oath. I then put my sword in the slight gap of the elevator's doors and opened it. "2B get in!!" with that said, she sprinted and jumped and grabbed the ladder going to the rooftop of the building. I followed her and took my sword which was holding the doors open, which resulted the elevator doors to close forcefully creating an ear piercing noise. The machine units couldn't get here anymore and we were safe. For now at least.

The yellow and red metal bars of the ladder were rusty. It had a high chance of breaking and it was a miracle that it could support both me and 2B's weight, my weight is 129.9 kg and 2B is 150 kg. As I was climbing up the ladder I looked up and saw something that made my pulse rate increase. "Warning: sudden increase in heart pulse and rise in body's temperature. Suggestion: undergo maintenance" Said Pod 153. "Shut up nothing's wrong!!" I said obviously sounding flustered. Then I noticed 2B stopping and looking down at me. "Is something wrong? Should I be concerned?" asked 2B. "O-o-oh n-never mind nothing is wrong continue climbing please. Ehehe" with that said she continued climbing up the ladder and soon enough we reached the rooftop of the building.

As we reached the rooftop we both took a break and underwent maintenance and took a bit of rest. Once I was done I looked over at 2B and saw that she was not done with her maintenance. I took that extra time to my advantage and looked around my surroundings and the scenery. The rooftop that we were currently standing on, was mostly covered by plant roots and stem. There was another building that was crashed into this one which gave us a new escape route from the machines below. Not that they could come up here or climb the ladder anyway. The tunnel also was too narrow for flying machine units to hover up here. Once I made sure that we could escape the building and head over to another area, I took a moment to look at City Ruins from this skyscraper. Honestly watching the city ruins both amazed me and saddened me. Saddened because it made me wonder what terrible things have happened once humans lived on earth. Whatever it was, I can't imagine being in their place. I sound selfish for a supposed emotionless android. It amazed me because first; the plant and animal life taking over the city was simply spectacular. It really was something to behold. I went over the edge of the rooftop and felt the cooling wind on my skin. I then inhaled deeply and exhaled slowly. Feeling the adrenaline going through every fiber of my being.

Second; The scenery also made me hopeful and anxious at the same time. Once the machines were defeated, what would this city or the rest of the world would look like? Can us androids live together with humans in peace? Can we live a full happy life with our loved ones, experiencing every outcome of it, good or bad with them? These were the thoughts that motivated me to keep going. No matter what I kept going and hoping for a better future.

I was brought back from my thoughts when 2B was done with her maintenance and told me to get moving. She was heading towards a giant tree root that gave a clear path to the other building crashed over this one. But before she went any further I called her. There is something that I needed to discuss with her.

"Hold on 2B, before we go and look for other areas, I want to discuss something with you." I said stopping her from her track. "What is it that you want to discuss with me 9S?"She looked at me expectantly. Even though she was wearing her black visor, I could tell by her facial features. Just by looking at her my breath got taken and I started to feel my heart's pulse increase. The way she was standing showed off her elegant figure. Her body so delicate yet it could withstand almost anything. Her dress that showed off her slender legs. Her beautiful face with those rosy lips and that unique mole. Her stormy blue eyes which were covered by that visor. Everything about her was perfect. Suddenly I had trouble talking. My pulse was drastically increasing and I could notice the temperature of my body going higher.

"Well, what is it?" asking 2B while she was impatiently tapping her foot. I then realized that I've been staring at her. "uhhh. R-right, I wanted to thank you for saving me from that machine and I wanted to also apologize for causing you trouble." I said taking a slight bow. "It's nothing just pay more attention to your surroundings next time." Said 2B with what looked like an amused expression. " And another thing, I don't know if you noticed it but while we were surrounded by those machines, some of them kept saying something strange and out of the ordinary. They kept repeating 'Seven-sama'." With that said all the hint of an amused expression she wore on her face drained and was taken over by seriousness again. " I see. And are you certain of this discovery?' asked 2B with a stern tone. "Yes. I'm positive." I confirmed and she immediately contacted her operator 6O.

"This is operator 6O. Is there anything I can do for you 2B?" asked operator 6O in her cheerful voice. "Operator 6O, connect me to the commander immediately. I have an emergency news" said 2B but her request was denied by 6O saying that the commander wasn't available at the moment. "maybe you can leave a message to me and I will report it to the commander as soon as I see her." Suggested 6O and 2B complied. 2B then informed 6O about their recent discovery they made regarding the former operator Seven and the weird behavior of the machines repeating his name and adding the suffix same at the end of it.

 **_Somewhere in the Sewers_**

"AAaaaaahhhhh!!!" screamed Seven in pain as his arms were replaced by a combat type machine. " This will do, with this I will take my revenge and the possibility of my success increases." He said gripping and flexing his new hands and arms. He walked over the dead corpse of the machine and picked it up. Then he headed to the central point of the sewer system were other tunnels also connected. In the middle there was a deep gap between each tunnel that led down deep into nothingness. Then he threw the machine and the machine fell towards its doom. It fell over a pile of dead android and machine corpses.

"HE…HEHEHE….HEHEHEHEHE…HAHAHAHAHA……..HAHAHAHAHAHAHAHAHAHAHAHAHAHAHA" laughed seven maniacally. "They will all pay" chuckled Seven as he went back to his business.

 **To Be Continued** **_ Thank you for following and favouriting my story. Also thank you for the review. If there are grammatical, Spelling or any other mistakes please do not hesitate to either review it in this story and tell my mistakes or pm me. See you guys next time and I hope you'll enjoy my story.** **Disclaimer: I do not own Nier Automata.**


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